Hi there, I need to translate some GFF3 (and/or BED) files from the chromosome co-ordinates used in the current S. cerevisiae assembly (circa 2011) back into the co-ordinates for the SacCer2 assembly (June 2008). This is because all the rest of the data I'm analysing are aligned to the (older) SacCer2 assembly.
The datasets are the ribosomal profiling data from Ingolia et al. (2009). The raw files are available via SGD in both GFF3 and BED format: http://downloads.yeastgenome.org/published_datasets/Ingolia_2009_PMID_19213877/track_files/ I know I can use liftOver to convert co-ordinates in a GFF3/BED file using a chain file that maps the co-ordinates of one assembly to another. However I didn't find any such chain files here: http://hgdownload.cse.ucsc.edu/downloads.html#yeast In addition the online version: http://genome.ucsc.edu/cgi-bin/hgLiftOver appears to allow you to convert from old assemblies (e.g. SacCer2) to new assemblies (e.g. SacCer3), but not the other way around. I need to do this because the new Ingolia data is aligned (presumably) to the most recent assembly (see link above), but I need it in SacCer2 co-ords. As suggested on http://genome.ucsc.edu/FAQ/FAQdownloads.html I am e-mailing you to request a generation of such an over.chain file. Best regards, Alex -- Alex Lancaster, Ph.D. Whitehead Institute for Biomedical Research _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
